I am currently trying to analyze my single cell RNA-seq sample generated from 10X Genomics Chromium. After the data was collected, I start off by running Cell Ranger pipeline to see if I could assign cell types for each cluster of cells, however, the tSNE does not seem to provide a clear-cut on different clusters due to the relatively low number of genes that have low enough p-values. Thus I turned my head to Seurat, which seems to be utilized by more research.
What is interesting, is that following by the tutorial from Satija Lab web page, I have A LOT more statistically significant differentially expressed genes in each cluster running tSNE.
So here is my question, what is the difference between Seurat and Cell Ranger in processing the data? Are they different in normalization or filtering? If not, what may lead to different yield in my case?
If it helps, my sample was collected from APL patients. I am specifically looking at myeloblasts and their possible lineage in the bone marrow. I am not sure if I should post the result from two approaches but if it helps, I will post it here.
Thank you all in advance, BC